ibdsegments

1.0.1

Identity by Descent Probability in Pedigrees

0packages depend

2Kdownloads / year

61.5%test coverage

13/13checks pass

Overview

About

Maintained by Maarten KruijverFirst published 2025-05-021 releasesCRAN page ↗

Identity by Descent (IBD) distributions in pedigrees. A Hidden Markov Model is used to compute identity coefficients, simulate IBD segments and to derive the distribution of total IBD sharing and segment count across chromosomes. The methods are applied in Kruijver (2025) doi:10.3390/genes16050492. The probability that the total IBD sharing is zero can be computed using the method of Donnelly (1983) doi:10.1016/0040-5809(83)90004-7.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("ibdsegments", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ibdsegments

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-ibdsegments

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ibdsegments

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.21

61.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 431 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 12%

Downloads

CRAN downloads in the past year

Rank #21,901 · ~5/day · ~164/mo

Releases R versions

Daily download trend is not available in this view yet.

20030 days

51790 days

2K1 year

Compare downloads with other packages →

Also on410 r2u32 autocran

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

Rcpp pedtools expm

LinkingTo (1)

Rcpp

Suggests (3)

testthat ribd ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Maarten Kruijver

Author, Maintainer

Authors (1)

Maarten Kruijver

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-02
Total releases: 1 / 1 yrs
License: GPL (>= 2) OSI
Download size: 279 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →